def test():
# TESTS
ncbi.get_sp_lineage("9606")
t = ncbi.get_topology([9913,31033,7955,9606,7719,9615,44689,10116,7227,9031,13616,7165,8364,99883,10090,9598])
ncbi.annotate_tree(t)
print t.get_ascii(show_internal=True, compact=False)
t.show()
def test():
# TESTS
ncbi.get_sp_lineage("9606")
t = ncbi.get_topology([
9913, 31033, 7955, 9606, 7719, 9615, 44689, 10116, 7227, 9031, 13616,
7165, 8364, 99883, 10090, 9598
])
ncbi.annotate_tree(t)
print t.get_ascii(show_internal=True, compact=False)
t.show()
def annotate_tree_with_taxa(t, name2taxa_file, tax2name=None, tax2track=None):
if name2taxa_file:
names2taxid = dict(
[map(strip, line.split("\t")) for line in open(name2taxa_file)])
else:
names2taxid = dict([(n.name, n.name) for n in t.iter_leaves()])
not_found = 0
for n in t.iter_leaves():
n.add_features(taxid=names2taxid.get(n.name, 1))
n.add_features(species=n.taxid)
if n.taxid == 1:
not_found += 1
if not_found:
print >> sys.stderr, "WARNING: %s nodes where not found within NCBI taxonomy!!" % not_found
return ncbi.annotate_tree(t, tax2name, tax2track)
def annotate_tree_with_taxa(t, name2taxa_file, tax2name=None, tax2track=None):
if name2taxa_file:
names2taxid = dict([map(strip, line.split("\t"))
for line in open(name2taxa_file)])
else:
names2taxid = dict([(n.name, n.name) for n in t.iter_leaves()])
not_found = 0
for n in t.iter_leaves():
n.add_features(taxid=names2taxid.get(n.name, 1))
n.add_features(species=n.taxid)
if n.taxid == 1:
not_found += 1
if not_found:
print >>sys.stderr, "WARNING: %s nodes where not found within NCBI taxonomy!!" %not_found
return ncbi.annotate_tree(t, tax2name, tax2track)